Bioinformatics – Lecture Notes

Class 1

1. Go over Syllabus
2. Get class list and backgrounds
3. Check if any other possible class time.
4. Go over NIH working definition of Bioinformatics and Computational Biology

NIH has a Bioinformatics Web Page

The Biomedical Information Science and Technology Initiative (BISTI)

http://grants.nih.gov/grants/bistic/bistic.cfm

5. Introduction to Bioinformatics

Types of Data –

Biological

Medical

Behavorial

Health

Bioinformatics encompasses a huge variety of areas.

Data Acquisition

Data Organization

Data Archives

Data Analysis

Data Visualization

6. Examples of Initiatives/Projects

Human Genome Project

 http://www.ornl.gov/hgmis/

Begun in 1990, the U.S. Human Genome Project is a 13-year effort

coordinated by the Department of Energy and the National
Institutes of Health. The project originally was planned to last 15
years, but effective resource and technological advances have
accelerated the expected completion date to 2003. Project goals are
to

• identify all the approximately 30,000 genes in human DNA,

• determine the sequences of the 3 billion chemical base
pairs that make up human DNA,
• store this information in databases,
• improve tools for data analysis,
• transfer related technologies to the private sector, and
• address the ethical, legal, and social issues (ELSI) that may
arise from the project.

Several types of genome maps have already been completed, and a

working draft of the entire human genome sequence was
announced in June 2000, with analyses published in February
2001. An important feature of this project is the federal
government's long-standing dedication to the transfer of
technology to the private sector. By licensing technologies to
private companies and awarding grants for innovative research, the
project is catalyzing the multibillion-dollar U.S. biotechnology
industry and fostering the development of new medical
applications.

The Visible Human Project®

http://www.nlm.nih.gov/research/visible/visible_human.html

The Visible Human Project® is an outgrowth of the NLM's 1986

Long-Range Plan. It is the creation of complete, anatomically
detailed, three-dimensional representations of the normal male and
female human bodies. Acquisition of transverse CT, MR and
cryosection images of representative male and female cadavers has
been completed. The male was sectioned at one millimeter
intervals, the female at one-third of a millimeter intervals.

The long-term goal of the Visible Human Project® is to produce a

system of knowledge structures that will transparently link visual
knowledge forms to symbolic knowledge formats such as the
names of body parts.
The Virtual Human Project – It is not just the NIH

http://vhgallery.gsm.com/

Images and animations made with their specified software are

deposited at the site and are published for use by educators,
students, healthcare professionals, publishers, and anyone else
needing high-quality anatomical imagery. Over time, they expect
the site to become a comprehensive collection that will rival the
best of traditional anatomy publications.

Human Brain Project

http://www.nimh.nih.gov/neuroinformatics/index.cfm

The Human Brain Project is a broad-based initiative which

supports research and development of advanced technologies, and
infrastructure support, through cooperative efforts among
neuroscientists and information scientists (computer scientists,
engineers, physicists, and mathematicians). The goal is to produce
new digital capabilities providing a World Wide Web (WWW)
based information management system in the form of interoperable
databases, and associated data management tools. Tools would
include, and are not limited to, graphical interfaces, querying and
mining approaches, information retrieval, data analysis,
visualization and manipulation, integrating tools for data analysis,
biological modeling and simulation, and tools for electronic
collaboration. The Neuroscience database will be interoperable
with other databases, such as genomic and protein databases, to
create the capability to analyze functional interactions in greater
depth. Tools will also need to be created to manage, integrate and
share this resource via the WWW providing the capability for
channels of communication and collaboration between
geographically distinct sites. These databases and tools will be
used by neuroscientists, behavioral scientists, clinicians and
educators, in their respective fields, to understand brain structure,
function, and development across the many levels and areas of data
collection and analysis.

The Physiome Project

http://www.physiome.org/frontpage.html

The PHYSIOME PROJECT is an integrated multi-centric program

to design, develop, implement, test and document, archive and
 disseminate quantitative information and integrative models of the
functional behavior of organelles, cells, tissues, organs, and
organisms. The long-range goal is to understand and describe the
human organism, its physiology and pathophysiology, and to use
this understanding in improving human health. but much or most
of what must be learned will come from other species. The project
aims toward providing models that summarize information on
physiological systems, integrating the observations from many
laboratories into quantitative, self-consistent, comprehensive
descriptions. The goal is to provide to the community of scientists,
physicians, teachers, and to medical health professional and
industrial communities, functional descriptions of human
biological systems in health and disease. A fundamental and major
feature of the program is the databasing of the basic observations
for retrieval and evaluation.

The Rice Genome Project

http://genome.sinica.edu.tw/

An international rice genome sequencing project, IRGSP, is

initiated three years ago, and the primary goal is the complete
sequence of rice. The reasons people choose rice as the material as
the first crop for genome sequencing project are: (1) rice is an
important crop in the world; (2) the genome size of rice is 430 Mb,
the smallest one among crops; (3) linkage maps and physical maps
of rice have been established and many EST sequences have been
registered; (4) the transgenic rice technology has been established;
(5) rice shares a co-linear gene organization with other cereal
grasses, thus rice is a key to knowledge of the genomic
organization of the other grasses.

The Human Proteome Organization (HUPO) – “genes were easy”

http://www.healthtech.com/2001/hpr/hpr_pressrelease.htm

Proteomics is in essence the study of the function,

regulation and expression of proteins in relation to the
normal function of the cell and in the initiation or
progression of a disease state. Proteomics is of particular
importance as it is at the level of protein activity that most
diseases are manifested. Consequently proteomics seeks to
correlate directly the involvement of specific proteins and
/or protein complexes in a given disease state.

The applications for proteomics are considerable:-

 • Specific proteins can be identified as highly
accurate and sensitive markers for disease at a very early
stage of onset, thus ensuring their utility in a diagnostic
capacity.
• Proteins are important in the prognosis and in the
monitoring of therapeutic treatments, as the under or over
expression of proteins identified as being disease markers
reduces with the improvement in a disease condition. An
important potential application here is in increasing the
speed and efficacy of clinical trials.
• A knowledge of protein expression patterns can
provide insight into potential toxic side-effects during drug
screening and lead optimisation.
• Proteins identified as being relevant in specific
disease conditions could be valid targets for therapeutic
agents and thus could have an important role in the
development of new therapeutic treatments.

7. Course Overview

This course will focus on a small subset of bioinformatics – computational

molecular biology. This covers areas such as sequence alignment,
evolutionary trees, protein structural prediction, and transcription data
analysis (microarray analysis). For many, when using the term
bioinformatics, this is what they mean. At present, in industry, there is a
huge demand for people trained in these areas. Hence, the course will
focus on these areas.

The National Center for Biotechnology Information (NCBI) has tools and
databases for bioinformatics.

http://www.ncbi.nlm.nih.gov/

8. Biological References

1. Molecular Biology of the Cell by Bruce Alberts (1994)

2. Molecular Cell Biology by Harvey Lodish, Arnold Berk, S. Lawrence
Zipursky, and Paul Matsudaira (1999)